Is it possible to generate an .exe file from an existing Unity exported application?

Let’s say we have an Origin.exe, it is made and exported by Unity. When we open Origin.exe, it shows an empty scene. We can do some modification on this scene, like adding a box and so on. Finally, we should be able to export the modified scene. So ,can I use code in Origin.exe to generate another Scene.exe?

No you can’t !
The .exe is an executable format. This is the format that is understood by Windows operating system. If you want to modify changes in a Unity Scene, you need to provide in a format that Unity Understand.
The Executable format is for the debug or release. All changes you make in a scene at run time will vanish when you quit the game unless you have a mechanism to have them stored persistently.